ArticlePloS one2015
Genome-wide SNP identification and characterization in two soybean cultivars with contrasting Mungbean Yellow Mosaic India Virus disease resistance traits.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed, 44 citations in OpenAlex.
- CRISPR/Cas9 in soybean research: a measured leap toward genetic refinement.Frontiers in genome editing · 2026Review
- Allelic differences within DNA polymerase delta subunit 1 correlate with geminivirus resistance in diverse plants.G3 (Bethesda, Md.) · 2025Article
- Identification and fine-mapping of novel major locus for yellow mosaic disease resistance in Glycine soja.Plant cell reports · 2025Article
- Proposed EU NGT legislation in light of plant genetic variation.Plant biotechnology journal · 2025Review
- Genome-Wide Identification and Characterization of SNPs and InDels ofPlants (Basel, Switzerland) · 2024Article
- Identification of sex-specific markers using genome re-sequencing in the blunt snout bream (Megalobrama amblycephala).BMC genomics · 2024Article
- Whole-genome resequencing of common bean elite breeding lines.Scientific reports · 2023Article
- The rising threat of geminiviruses: molecular insights into the disease mechanism and mitigation strategies.Molecular biology reports · 2023Review
- A source of resistance against yellow mosaic disease in soybeans correlates with a novel mutation in a resistance gene.Frontiers in plant science · 2023Article
- Genome-wide identification and development of InDel markers in tobacco (Physiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Whole Genome Re-sequencing of Soybean Accession EC241780 Providing Genomic Landscape of Candidate Genes Involved in Rust Resistance.Current genomics · 2020Article
- Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset.BMC genomics · 2020Article
- Article
- Genome-wide analysis of genetic variations between dominant and recessive NILs of glanded and glandless cottons.Scientific reports · 2019Article
- Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits.BMC plant biology · 2018Article
- Uncovering SNP and indel variations of tetraploid cottons by SLAF-seq.BMC genomics · 2017Article
- Linkage mapping ofBreeding science · 2017Article
- Whole-Genome Characteristics and Polymorphic Analysis of Vietnamese Rice Landraces as a Comprehensive Information Resource for Marker-Assisted Selection.International journal of genomics · 2017Article
- Identification of Sesame Genomic Variations from Genome Comparison of Landrace and Variety.Frontiers in plant science · 2016Article
- Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant ofInternational journal of plant genomics · 2016Article
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Authors and funding
7 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mungbean yellow mosaic India virus (MYMIV) is a bipartite Geminivirus, which causes severe yield loss in soybean (Glycine max). Considering this, the present study was conducted to develop large-scale genome-wide single nucleotide polymorphism (SNP) markers and identify potential markers linked with known disease resistance loci for their effective use in genomics-assisted breeding to impart durable MYMIV tolerance. The whole-genome re-sequencing of MYMIV resistant cultivar 'UPSM-534' and susceptible Indian cultivar 'JS-335' was performed to identify high-quality SNPs and InDels (insertion and deletions). Approximately 234 and 255 million of 100-bp paired-end reads were generated from UPSM-534 and JS-335, respectively, which provided ~98% coverage of reference soybean genome. A total of 3083987 SNPs (1559556 in UPSM-534 and 1524431 in JS-335) and 562858 InDels (281958 in UPSM-534 and 280900 in JS-335) were identified. Of these, 1514 SNPs were found to be present in 564 candidate disease resistance genes. Among these, 829 non-synonymous and 671 synonymous SNPs were detected in 266 and 286 defence-related genes, respectively. Noteworthy, a non-synonymous SNP (in chromosome 18, named 18-1861613) at the 149th base-pair of LEUCINE-RICH REPEAT RECEPTOR-LIKE PROTEIN KINASE gene responsible for a G/C transversion [proline (CCC) to alanine(GCC)] was identified and validated in a set of 12 soybean cultivars. Taken together, the present study generated a large-scale genomic resource such as, SNPs and InDels at a genome-wide scale that will facilitate the dissection of various complex traits through construction of high-density linkage maps and fine mapping. In the present scenario, these markers can be effectively used to design high-density SNP arrays for their large-scale validation and high-throughput genotyping in diverse natural and mapping populations, which could accelerate genomics-assisted MYMIV disease resistance breeding in soybean.
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